Medicine
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This repository contains the published and unpublished research of the Faculty of Medicine by the staff members of the faculty
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Item Development of a low cost semiquantitative polymerase chain reaction assay for molecular diagnosis of williams syndrome(Clinical Laboratory Publications, 2024) Ranaweera, D.M.; de Silva, D.C.; Samarasinghe, D.; Perera, S.; Kugalingam, N.; Samarasinghe, S.R.; Madushani, W.Y.; Jayaweera, H.H.E.; Gunewardene, S.; Muneeswaran, K.; Gnanam, V.S.; Chandrasekharan, N.V.BACKGROUND: Williams Beuren Syndrome (WBS) is a well-recognized and common genetic cause of congenital heart defects, developmental delay, hypercalcemia, and characteristic facial features. It is caused by a 1.5 - 1.8 Mb heterozygous deletion of chromosome 7q11.23 with loss of around 28 coding genes. The aim of this study was to develop a low-cost, semi-quantitative PCR (sqPCR) method to detect the chromosome 7q11.23 deletion. METHODS: Twenty-four suspected WBS cases were recruited following ethical clearance and informed consent. Blood was obtained, DNA extracted and spectrophotometrically quantified using standard methods. To detect the deletion by dosage analysis, a target region within a gene located in the WBS commonly deleted region of 7q11.23 was amplified together with a control region in a duplex sqPCR assay. The control region was telomeric to the WBS commonly deleted region and was located in chromosome 7q31.2. The two target regions within the deleted region namely a locus within ELN and a marker in the intergenic region between FZD9 and FKBP6 and designated IFF, were amplified in separate duplex sqPCR assays. The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene was used as the control for normalization. Included in the assay were a non-deleted and deleted individuals' samples. RESULTS: Nineteen patients were identified to have the deletion while five did not. All 24 patients' results were confirmed by whole exome sequencing and 11 also by fluorescence in-situ hybridization (FISH). CONCLUSIONS: The data obtained indicates the sqPCR assay developed in this study to be an accurate and reliable diagnostic test for WBS. Most Sri Lankan patients with WBS are diagnosed clinically, as many parents of affected WBS children are unable to afford currently available molecular diagnostic testing. This low cost sqPCR test is therefore likely to benefit Sri Lankan WBS patients, by enabling genetic testing for confirming or refuting a clinical diagnosis of WBS and may be of use in other low and middle income countries.Item Genome organization, in-silico structure, and cellular localization of putative lipid transporter, ARV1 from parasitic nematode Setaria digitata(Elsevier Inc., 2022) Wickramatunga, P.G.T.S.; Gunawardene, Y.I.N.S.; Chandrasekharan, N.V.; Dassanayake, R.S.Setaria digitata, a nematode that lives in the peritoneal cavity of ruminants is the causative agent of cerebrospinal nematodiasis affecting livestock health. The ‘ACAT related enzyme 2 required for viability 1’ (arv-1) gene encodes putative lipid transporter that is essential in eukaryotes. The molecular characterization of nematode arv-1 has scarcely been studied and putative arv-1 isolated from S. digitata was used for this purpose. Docking and computer simulation studies using a modeled 3D structure of S. digitata ARV1 (Sd-ARV-1) with ceramide ligands revealed that the amino acid residues, Ile182, Leu56, Ala61, Gln186 and Gln146 are likely involved in the formation of potential sphingolipid binding sites having the same conserved residues in other nematodes. Sd-arv-1, a single copy gene, genomic region (1676 bp) had five exons encoding 217 amino acids, being interspersed by four introns showing a similar gene organization to other nematodes. Sd-ARV-1 is expressed ubiquitously at all development stages of the S. digitata life cycle. Tissue localization analyses revealed that Sd-ARV-1 was significantly expressed in the longitudinal muscle layer, endodermis, uterine wall, eggs, growing embryos inside the uterus, microfilariae, intestinal wall, esophagus lumen, dorsal nerve cord and ventral nerve cord. Therefore, ARV1 is a structurally conserved, ubiquitously expressed protein, which may be involved in development, reproduction, tissue remodeling, muscle contraction etc., in nematodes.Item Reconstruction of Metabolic Pathways for the Setaria digitata Whole Genome(Sri Lanka Medical Association, 2020) Rashanthy, N.; Kothalawala, M.S.A.; Mugunamalwaththa, T.S.; Darshika, W.A.S.; Lakmali, G.L.Y.; de Zoysa, K.; Chandrasekharan, N.V.; Gunawardene, Y.I.N.S.; Suravajhala, P.; Dassanayake, R.S.INTRODUCTION AND OBJECTIVES: Setaria digitata is a Wolbachia-free filarial parasite that resides in the abdominal cavity of ungulates. It can cause cerebrospinal nematodiasis (CNS) in unnatural hosts such as sheep, goats, which causes a serious threat to livestock farming. Furthermore, S. digitata can also infect humans causing several conditions showing a gradual adaption to humans. METHODS: Despite, to date, complete a metabolic pathway reconstruction of S. digitata has not been undertaken and therefore, in this study the latter analyses were carried out using BLAST2GO software. RESULTS: Metabolic pathway analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) database identified 111 enzymes found in total of 246 contigs that involve in 95 metabolic pathways, in which the most over-represented pathways are Biosynthesis of antibiotics, Phosphatidylinositol signaling system and Purine metabolism. Since S. digitata does not harbor Wolbachia endosymbiont, it was theorized that the S. digitata genome must encodes genes to carryout haem, riboflavin and nucleotides pathways, otherwise encoded by Wolbachia genome, potentially through lateral transfer of Wolbachia to an ancestor of S.digitata. Here, KEGG analysis identified 16 enzyme coding genes involve in nucleotide biosynthesis and one enzyme involve in riboflavin biosynthesis pathway. Although studies have revealed that FAD and glutathione pathways are complete in all nematode genomes, the genes encoding FAD and glutathione pathways were not found in the S. digitata. Moreover, complete nucleotide synthesis pathway and haem synthesis pathway were not found. CONCLUSION: This suggests that S. digitata may have evolved its own sequences to encode those biosynthetic pathways and hence calling for investigations to undertake characterization of genes involved in these pathways.Item Molecular diagnosis of velo-cardio-facial syndrome among sri lankan patients with congenital cardiac defects(Sri Lanka College of Paediatricians, 2015) Tevarajan, I.; Ranaweera, D. M.; Perera, S.; Samarasinghe, D.; Morawakkorala, R.; Silva, R. L.; de Silva, D.; Chandrasekharan, N.V.Velo cardio facial Syndrome (VCFS) is caused by a 3 Mb deletion of chromosome 22qll.2. Its multiple clinical features include orofacial clefting, congenital cardiac defects (especially conotruncal),developmental delay and learning difficulties. Hypoparathyroidism and thymic hypoplasia are associated. Dysmorphic features include expressionless face, prominent nose, narrow eyes and long fingers/ toes. Clinical diagnosis is difficult due to its variability making molecular diagnosis essential but this is often too expensive for widespread use. We have developed a less expensive semi-quantitative PCR method for diagnosing VCFS and report preliminary results in congenital cardiac defect patients.OBJECTIVE: • Identify the 22qll.2 deletion syndrome among a selected group of children with typical cardiac defects • Describe clinical features of affected cases DESIGN, SETTING AND METHOD: TweIve children (6 males, mean age 3y lmo) with conotruncal congenital cardiac anomalies or cardiac defects associated with other clinical feature of VCFS were .recruited following informed consent from parents. Ethical approval had been granted for this study. A blood sample was obtained for DNA extraction and the clinical data recorded. Molecular diagnosis was performed using semi-quantitative PCR. RESULTS: Three cases were positive for the deletion. Their cardiac anomalies were an interrupted aortic arch,tetralogy of Fallot and right sided aortic arch. None had palatal anomalies and two (67%) had learning difficulties. None had a positive family history. Only one had facies that were typical. The negative cases included six with aortic arch anomalies, none with clefting and 4 with learning difficulties(44). Two had a family history suggestive of VCFS and two had typical facial features. CONCLUSIONS: Three out of the 12 children were positive for the 22qll.2 deletion.Item Development of siRNA mediated RNA interference and functional analysis of novel parasitic nematode-specific protein of Setaria digitata(Academic Press, 2018) Somarathne, M.B.C.L.; Gunawardene, Y.I.N.S.; Chandrasekharan, N.V.; Dassanayake, R.S.Despite the differences of the host, parasitic nematodes may share commonalities in their parasitizing genes. Setaria digitata novel protein (SDNP) is such an entity which is parasitic nematode-specific and having sequence similarities with those of W. bancrofti, B. malayi, Loa loa and Onchocerca volvulus. Post-transcriptional gene silencing by siRNA mediated RNA interference (RNAi) is a widely used technique in functional genomics. Though the technique has been used in several free-living, plant and animal parasitic nematodes, it has not yet been tried out for the filarial worm S. digitata. In this study, we developed an effective siRNA delivery method by microinjection and utilized the siRNAi tool to knockdown SDNP to study the phenotypic and cellular changes associated with the interference. qPCR analysis revealed, a significant reduction of SDNP transcript levels following siRNA microinjection into S. digitata adult worms. Similarly, immunohistochemical staining indicated a reduction of SDNP protein expression. Furthermore, worms treated with siRNA showed a significant reduction of microfilariae release together with embryonic lethality by arresting an early developmental stage compared to non-treated worms. A distinct motility reduction was also observed in treated worms compared to non-treated counterparts. This is the first report of the amenability of S. digitata to the siRNA induced RNAi. The presence of inter-domain linkers of muscle-specific twitchin kinase and calcium-dependent protein kinase isoform CDPK1 together with what our results revealed suggest that SDNP is most likely a protein involved in muscle movement and growth and development of the nematode. Hence SDNP has the characteristics of a potential drug target.Item Modified mismatch polymerase chain reaction-restriction fragment length polymorphism detected mutations in codon 12 and 13 of exon 2 of K-ras gene in colorectal cancer patients and its association with liver metastases: Data from a South Asian country(Medknow Publications, 2016) Faleel, F.D.; Zoysa, M.I.; Lokuhetti, M.D.; Gunawardene, Y.I.N.S.; Chandrasekharan, N.V.; Dassanayake, R.S.AIM: Mutations in K-ras codon 12 and 13 of exon 2 are known to affect prognosis and impart resistance to anti-epidermal growth factor monoclonal antibody therapy in colorectal carcinoma (CRC). Our aim was to investigate the utility value of modified mismatch polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay to detect mutation in K-ras codons of CRC patients and to relate the mutational status to liver metastasis. METHODOLOGY: Mismatch PCR-RFLP was developed to detect K-ras mutations in DNA isolated from paraffinized tumor tissue of thirty CRC patients. All patients had 5 year follow-up data to detect liver metastasis. Cross-tabulations were generated between K-ras mutations and the metastatic status. The Chi-square test was used to indicate statistical significance of the association. RESULTS: Of the 30 CRC patients investigated, K-ras mutations of codons 12 and/or 13 of exon 2 were detected in 14 (46.6%). Meanwhile, 13 patients (43.3%) were observed to have developed liver metastases. There was a significant association between the presence of the K-ras mutation in codon 12 and the occurrence of liver metastasis (χ2 = 4.693, P = 0.030) on the contrary to the mutation in codon 13 to which such occurrence of liver metastases was not seen (χ2 = 1.884, P = 0.169). CONCLUSION: Codon 12 of exon 2 of K--ras gene detected by modified mismatch PCR-RFLP assay is significantly associated with liver metastasis in CRC patients during the first 5 years after surgery. Thus, modified mismatch PCR-RFLP protocol is a suitable method in this setting to detect K-ras gene mutations predicting liver metastasis in CRC patients.Item Application of a real time Polymerase Chain Reaction (PCR) assay for the early diagnosis of human leptospirosis in Sri Lanka(Academic Press, Elsevier, 2016) Denipitiya, D.T.H.; Chandrasekharan, N.V.; Abeyewickreme, W.; Hartskeerl, C.M.; Hartskeerl, R.A.; Jiffrey, A.M.; Hapugoda, M.D.Leptospirosis has a major impact on health in Sri Lanka but is probably grossly under-recognized due to difficulties in clinical diagnosis and lack of diagnostic laboratory services. The objective of this study was to establish and evaluate a SYBR Green-based real-time Polymerase Chain Reaction (rt-PCR) assay for early, rapid and definitive laboratory diagnosis of leptospirosis in Sri Lanka. The rt-PCR assay was established and analytical specificity and sensitivity were determined using reference DNA samples. Evaluation of the assay for diagnosis of clinical samples was performed using two panels of serum samples obtained from 111 clinically suspected adult patients. Patients were confirmed as leptospirosis (n = 65) and non-leptospirosis (n = 30) by the Patoc - MAT. Other 16 samples gave ambiguous results. The analytical sensitivity of the rt-PCR was approximately 60 genome copies and no cross-reactivity was observed with saprophytic Leptospira spp. and other pathogenic microorganisms. Based on confirmation with Patoc-MAT on paired samples this corresponds to a diagnostic sensitivity and specificity of 67.7% (44/65) and 90.0% (27/30), respectively. This study showed that rt-PCR has the potential to facilitate rapid and definitive diagnosis of leptospirosis during early phase of infection in Sri Lanka.Item Molecular diagnosis of Williams Buren syndrome in a cohort of Sri Lankan patients(Sri Lanka Medical Association, 2012) Ranaweera, D.M.; de Silva, D.; Samarasinghe, D.; Perera, S.; Rajapaksha, N.; Chandrasekharan, N.V.INTRODUCTION: Williams Bueren Syndrome (WBS) is a common genetic cause of congenital heart defects associated with developmental delay, hypercalcaemia and characteristic facial dysmorphism. It is caused by a 1.5 to 1.8 Mb deletion of chromosome 7qll.23 involving the loss of around 23 genes including the elastin (ELN) gene. This study reports the development of a semi quantitative PCR method to diagnose WBS. AIMS: To establish a molecular diagnostic test for WBS and determine the frequency of ELN deletions among clinically suspected cases. METHODS: Sixteen suspected WBS cases identified by two paediatric cardiologists were recruited following ethical clearance and informed consent. DNA was extracted and dosage analysis was carried out using semi-quantitative PCR. In a multiplex PCR reaction normal (N), positive control (with a confirmed deletion) and patients' (PJ DNA was amplified using 2 primer pairs which amplified regions within the ELN gene and the CFTR gene on chromosome 7 but outside the deleted region. Following agarose gel electrophoresis, the amplified products were quantified. A ratio of P:N of 0.5 indicated the presence of a deletion while a ratio of 1 indicated the absence of a deletion. RESULTS: Among sixteen suspected cases, 12 (75%) had an ELN gene deletion while 4 cases did not. CONCLUSIONS: This semi-quantitative PCR method was able to distinguish ELN deleted cases from the non deleted ones. The preliminary data supports this as a useful diagnostic test for WBS but validation is required before its clinical use.Item Designing of immunogenic peptides from Dengue Virus NS1 region for production of monoclonal antibodies as diagnostic intermediates(Molecular Medicine Unit, Faculty of Medicine, University of Kelaniya, Sri Lanka, 2015) Munasinghe, M.M.E.; Chandrasekharan, N.V.; Korbakis, D.; Soosaipillai, A.; Diamandis, E.P.; Athapaththu, A.M.M.H.; Gunathilaka, P.A.D.H.N.; Abeyewickreme, W.BACKGROUND: Small peptide antigens have become an essential tool for antibody production in the recent life science research applications. The immunogenicity of peptide antigens is a critical factor to induce the immune response in order to produce desired antibodies. METHODS: In the current study, we have previously determined four Dengue (DEN) serotype specific peptides, containing 28 Amino Acid (AA) residues were re-designed. The peptides were re-designed considering many factors, for instance, sequence of the Sri Lankan isolates, abundance of Cysteine residues, solubility and the length of the peptide, carrier protein to be used and several other factors such as the N-terminal and C- terminal AAs and multiple AA residues. The peptide sequences were analysed using Antigen Profiler Peptide Tool (Thermo-scientific), Peptide Property Calculator (Genscript) and Swiss-Model (Biozentrum). RESULTS: The protein sequence of the peptides were changed according to the Sri Lankan isolates (AEB98757.1, ACS32038.1, AHG23239.1 and AHN50410.1). Oxidation of Cysteine residues results in significant conformational changes. Replacement of Cysteine with Serine prevents such oxidation reactions and it often retains full biological activity. Generally, peptides with a high number of hydrophobic AA (>50%) may result insoluble peptides. Similarly, to obtain a soluble peptide, it is important to contain at least one charged AA in every five AAs. Hence, the number of hydrophobic residues in the peptides were maintained below 50% and ensured that one out of every five amino acids is charged. The length of the peptide is an important factor as long peptide increases immunogenicity, but also increases the chance for cross-reactivity while a short peptide improves the specificity, but may not be immunogenic. In order to obtain both highly conserved and variable regions among four serotypes, the peptide length was determined as 29 residues. A terminal Cysteine was added to allow peptide conjugation with carrier protein. Keyhole Limpet Hemocyanin was selected as the carrier protein due to its higher immunogenicity. N-terminal Glutamine or Aspargine and C-terminal Proline or Glycine in the sequences were avoided. Finally, the peptides sequences were determined as: DEN1; CPESSDDQRA WNIWEVEDYGFGIFTTNIW,DEN2; CAESPN TNRA WNSLEVEDYGFGVFTTNIW, DEN3;CPESPSASRAWNVWEVEDYGFGVFTTNIW and .DEN4;CSESPNERRAWNSLEVEDYGFGMFTTNIW. CONCLUSION: These peptides have a high potential to be used as peptide antigens for Monoclonal Antibody production.Item Development of modified mismatch PCR-RFLP to screen mutations in codon 12 and 13 of K- ras gene of colorectal (CRC) patients in Sri Lanka(Sri lanka Medical Association, 2015) Dhilhani, M.F.F.; de Zoysa, M.I.M.; Chandrasekharan, N.V.; Gunawardene, Y.I.N.S.; Lokuhetti, M.D.S.; Dassanayake, R.S.INTRODUCTION AND OBJECTIVES: Mutations in K-ras codon 12, 13 of exon 2 are known to affect prognosis and impart resistance to anti EGFR monoclonal antibody therapy in CRC. Although several diagnostic tools have been developed for K-ras mutation testing, these procedures are too expensive or time consuming. Oufaim was to develop an effective, reliable and inexpensive method for the detection of K-ras mutations in codons 12 and 13 of exon 2 in CRC patients in Sri Lanka, and to relate the mutational status to liver metastasis, METHOD: The mismatch PCR-RFLP was developed and used to screen mutations in codon 12 and 13 for DMA isolated from paraffinized tumour tissue of 30 CRC patients followed up for 5 year after surgery to detect liver metastasis. Cross-tabulations were generated between K-ras mutations and the metastatic status. The Chi Square test was used to indicate statistical significance of the association. RESULTS: Analysis of banding pattern obtained from restriction digestion of PCR amplified region containing codon 12 and/or 13 of KRAS gene of 14(46.6%) CRC patients revealed the presence of mutations. Of the 30 patients, 13(43.3%) had developed liver metastases. There was a significant association between the presence of a K-ros mutation and the occurrence of liver metastasis (X2=4.693, p=0.003). CONCLUSION: This mismatch PCR-RFLP protocol is a suitable method to screen codon 12 and 13 mutation of K-ros gene to predict liver metastasis. Presence of these mutations is associated with the occurrence of liver metastasis during the first 5 years after surgery.